Daily Papers

The lack of annotated training data in bioacoustics hinders the use of large-scale neural network models trained in a supervised way. In order to leverage a large amount of unannotated audio data, we propose AVES (Animal Vocalization Encoder based on Self-Supervision), a self-supervised, transformer-based audio representation model for encoding animal vocalizations. We pretrain AVES on a diverse set of unannotated audio datasets and fine-tune them for downstream bioacoustics tasks. Comprehensive experiments with a suite of classification and detection tasks have shown that AVES outperforms all the strong baselines and even the supervised "topline" models trained on annotated audio classification datasets. The results also suggest that curating a small training subset related to downstream tasks is an efficient way to train high-quality audio representation models. We open-source our models at https://github.com/earthspecies/aves.

Recently, transformer-based models have demonstrated remarkable performance on audio-visual segmentation (AVS) tasks. However, their expensive computational cost makes real-time inference impractical. By characterizing attention maps of the network, we identify two key obstacles in AVS models: 1) attention dissipation, corresponding to the over-concentrated attention weights by Softmax within restricted frames, and 2) inefficient, burdensome transformer decoder, caused by narrow focus patterns in early stages. In this paper, we introduce AVESFormer, the first real-time Audio-Visual Efficient Segmentation transformer that achieves fast, efficient and light-weight simultaneously. Our model leverages an efficient prompt query generator to correct the behaviour of cross-attention. Additionally, we propose ELF decoder to bring greater efficiency by facilitating convolutions suitable for local features to reduce computational burdens. Extensive experiments demonstrate that our AVESFormer significantly enhances model performance, achieving 79.9% on S4, 57.9% on MS3 and 31.2% on AVSS, outperforming previous state-of-the-art and achieving an excellent trade-off between performance and speed. Code can be found at https://github.com/MarkXCloud/AVESFormer.git.

In the era of foundation models, achieving a unified understanding of different dynamic objects through a single network has the potential to empower stronger spatial intelligence. Moreover, accurate estimation of animal pose and shape across diverse species is essential for quantitative analysis in biological research. However, this topic remains underexplored due to the limited network capacity of previous methods and the scarcity of comprehensive multi-species datasets. To address these limitations, we introduce AniMer+, an extended version of our scalable AniMer framework. In this paper, we focus on a unified approach for reconstructing mammals (mammalia) and birds (aves). A key innovation of AniMer+ is its high-capacity, family-aware Vision Transformer (ViT) incorporating a Mixture-of-Experts (MoE) design. Its architecture partitions network layers into taxa-specific components (for mammalia and aves) and taxa-shared components, enabling efficient learning of both distinct and common anatomical features within a single model. To overcome the critical shortage of 3D training data, especially for birds, we introduce a diffusion-based conditional image generation pipeline. This pipeline produces two large-scale synthetic datasets: CtrlAni3D for quadrupeds and CtrlAVES3D for birds. To note, CtrlAVES3D is the first large-scale, 3D-annotated dataset for birds, which is crucial for resolving single-view depth ambiguities. Trained on an aggregated collection of 41.3k mammalian and 12.4k avian images (combining real and synthetic data), our method demonstrates superior performance over existing approaches across a wide range of benchmarks, including the challenging out-of-domain Animal Kingdom dataset. Ablation studies confirm the effectiveness of both our novel network architecture and the generated synthetic datasets in enhancing real-world application performance.

Neural posterior estimation (NPE), a type of amortized variational inference, is a computationally efficient means of constructing probabilistic catalogs of light sources from astronomical images. To date, NPE has not been used to perform inference in models with spatially varying covariates. However, ground-based astronomical images have spatially varying sky backgrounds and point spread functions (PSFs), and accounting for this variation is essential for constructing accurate catalogs of imaged light sources. In this work, we introduce a method of performing NPE with spatially varying backgrounds and PSFs. In this method, we generate synthetic catalogs and semi-synthetic images for these catalogs using randomly sampled PSF and background estimates from existing surveys. Using this data, we train a neural network, which takes an astronomical image and representations of its background and PSF as input, to output a probabilistic catalog. Our experiments with Sloan Digital Sky Survey data demonstrate the effectiveness of NPE in the presence of spatially varying backgrounds and PSFs for light source detection, star/galaxy separation, and flux measurement.

Federated Learning (FL) has gained significant attraction due to its ability to enable privacy-preserving training over decentralized data. Current literature in FL mostly focuses on single-task learning. However, over time, new tasks may appear in the clients and the global model should learn these tasks without forgetting previous tasks. This real-world scenario is known as Continual Federated Learning (CFL). The main challenge of CFL is Global Catastrophic Forgetting, which corresponds to the fact that when the global model is trained on new tasks, its performance on old tasks decreases. There have been a few recent works on CFL to propose methods that aim to address the global catastrophic forgetting problem. However, these works either have unrealistic assumptions on the availability of past data samples or violate the privacy principles of FL. We propose a novel method, Federated Orthogonal Training (FOT), to overcome these drawbacks and address the global catastrophic forgetting in CFL. Our algorithm extracts the global input subspace of each layer for old tasks and modifies the aggregated updates of new tasks such that they are orthogonal to the global principal subspace of old tasks for each layer. This decreases the interference between tasks, which is the main cause for forgetting. We empirically show that FOT outperforms state-of-the-art continual learning methods in the CFL setting, achieving an average accuracy gain of up to 15% with 27% lower forgetting while only incurring a minimal computation and communication cost.

The mixture of Expert (MoE) parallelism is a recent advancement that scales up the model size with constant computational cost. MoE selects different sets of parameters (i.e., experts) for each incoming token, resulting in a sparsely-activated model. Despite several successful applications of MoE, its training efficiency degrades significantly as the number of experts increases. The routing stage in MoE relies on the efficiency of the All2All communication collective, which suffers from network congestion and has poor scalability. To mitigate these issues, we introduce SMILE, which exploits heterogeneous network bandwidth and splits a single-step routing into bi-level routing. Our experimental results show that the proposed method obtains a 2.5x speedup over Switch Transformer in terms of pretraining throughput on the Colossal Clean Crawled Corpus without losing any convergence speed.

We consider a project (model) owner that would like to train a model by utilizing the local private data and compute power of interested data owners, i.e., trainers. Our goal is to design a data marketplace for such decentralized collaborative/federated learning applications that simultaneously provides i) proof-of-contribution based reward allocation so that the trainers are compensated based on their contributions to the trained model; ii) privacy-preserving decentralized model training by avoiding any data movement from data owners; iii) robustness against malicious parties (e.g., trainers aiming to poison the model); iv) verifiability in the sense that the integrity, i.e., correctness, of all computations in the data market protocol including contribution assessment and outlier detection are verifiable through zero-knowledge proofs; and v) efficient and universal design. We propose a blockchain-based marketplace design to achieve all five objectives mentioned above. In our design, we utilize a distributed storage infrastructure and an aggregator aside from the project owner and the trainers. The aggregator is a processing node that performs certain computations, including assessing trainer contributions, removing outliers, and updating hyper-parameters. We execute the proposed data market through a blockchain smart contract. The deployed smart contract ensures that the project owner cannot evade payment, and honest trainers are rewarded based on their contributions at the end of training. Finally, we implement the building blocks of the proposed data market and demonstrate their applicability in practical scenarios through extensive experiments.

Segmenting medical images is critical to facilitating both patient diagnoses and quantitative research. A major limiting factor is the lack of labeled data, as obtaining expert annotations for each new set of imaging data and task can be labor intensive and inconsistent among annotators. We present CUTS, an unsupervised deep learning framework for medical image segmentation. CUTS operates in two stages. For each image, it produces an embedding map via intra-image contrastive learning and local patch reconstruction. Then, these embeddings are partitioned at dynamic granularity levels that correspond to the data topology. CUTS yields a series of coarse-to-fine-grained segmentations that highlight features at various granularities. We applied CUTS to retinal fundus images and two types of brain MRI images to delineate structures and patterns at different scales. When evaluated against predefined anatomical masks, CUTS improved the dice coefficient and Hausdorff distance by at least 10% compared to existing unsupervised methods. Finally, CUTS showed performance on par with Segment Anything Models (SAM, MedSAM, SAM-Med2D) pre-trained on gigantic labeled datasets.

In the context of personalized federated learning (FL), the critical challenge is to balance local model improvement and global model tuning when the personal and global objectives may not be exactly aligned. Inspired by Bayesian hierarchical models, we develop a self-aware personalized FL method where each client can automatically balance the training of its local personal model and the global model that implicitly contributes to other clients' training. Such a balance is derived from the inter-client and intra-client uncertainty quantification. A larger inter-client variation implies more personalization is needed. Correspondingly, our method uses uncertainty-driven local training steps and aggregation rule instead of conventional local fine-tuning and sample size-based aggregation. With experimental studies on synthetic data, Amazon Alexa audio data, and public datasets such as MNIST, FEMNIST, CIFAR10, and Sent140, we show that our proposed method can achieve significantly improved personalization performance compared with the existing counterparts.

Clinical monitoring of metastatic disease to the brain can be a laborious and time-consuming process, especially in cases involving multiple metastases when the assessment is performed manually. The Response Assessment in Neuro-Oncology Brain Metastases (RANO-BM) guideline, which utilizes the unidimensional longest diameter, is commonly used in clinical and research settings to evaluate response to therapy in patients with brain metastases. However, accurate volumetric assessment of the lesion and surrounding peri-lesional edema holds significant importance in clinical decision-making and can greatly enhance outcome prediction. The unique challenge in performing segmentations of brain metastases lies in their common occurrence as small lesions. Detection and segmentation of lesions that are smaller than 10 mm in size has not demonstrated high accuracy in prior publications. The brain metastases challenge sets itself apart from previously conducted MICCAI challenges on glioma segmentation due to the significant variability in lesion size. Unlike gliomas, which tend to be larger on presentation scans, brain metastases exhibit a wide range of sizes and tend to include small lesions. We hope that the BraTS-METS dataset and challenge will advance the field of automated brain metastasis detection and segmentation.

We present Fox-1, a series of small language models (SLMs) consisting of Fox-1-1.6B and Fox-1-1.6B-Instruct-v0.1. These models are pre-trained on 3 trillion tokens of web-scraped document data and fine-tuned with 5 billion tokens of instruction-following and multi-turn conversation data. Aiming to improve the pre-training efficiency, Fox-1-1.6B model introduces a novel 3-stage data curriculum across all the training data with 2K-8K sequence length. In architecture design, Fox-1 features a deeper layer structure, an expanded vocabulary, and utilizes Grouped Query Attention (GQA), offering a performant and efficient architecture compared to other SLMs. Fox-1 achieves better or on-par performance in various benchmarks compared to StableLM-2-1.6B, Gemma-2B, Qwen1.5-1.8B, and OpenELM1.1B, with competitive inference speed and throughput. The model weights have been released under the Apache 2.0 license, where we aim to promote the democratization of LLMs and make them fully accessible to the whole open-source community.

Uncertainty Quantification (UQ) research has primarily focused on closed-book factual question answering (QA), while contextual QA remains unexplored, despite its importance in real-world applications. In this work, we focus on UQ for the contextual QA task and propose a theoretically grounded approach to quantify epistemic uncertainty. We begin by introducing a task-agnostic, token-level uncertainty measure defined as the cross-entropy between the predictive distribution of the given model and the unknown true distribution. By decomposing this measure, we isolate the epistemic component and approximate the true distribution by a perfectly prompted, idealized model. We then derive an upper bound for epistemic uncertainty and show that it can be interpreted as semantic feature gaps in the given model's hidden representations relative to the ideal model. We further apply this generic framework to the contextual QA task and hypothesize that three features approximate this gap: context-reliance (using the provided context rather than parametric knowledge), context comprehension (extracting relevant information from context), and honesty (avoiding intentional lies). Using a top-down interpretability approach, we extract these features by using only a small number of labeled samples and ensemble them to form a robust uncertainty score. Experiments on multiple QA benchmarks in both in-distribution and out-of-distribution settings show that our method substantially outperforms state-of-the-art unsupervised (sampling-free and sampling-based) and supervised UQ methods, achieving up to a 13-point PRR improvement while incurring a negligible inference overhead.

Large language models (LLMs) have surged in popularity and are extensively used in commercial applications, where the efficiency of model serving is crucial for the user experience. Most current research focuses on optimizing individual sub-procedures, e.g. local inference and communication, however, there is no comprehensive framework that provides a holistic system view for optimizing LLM serving in an end-to-end manner. In this work, we conduct a detailed analysis to identify major bottlenecks that impact end-to-end latency in LLM serving systems. Our analysis reveals that a comprehensive LLM serving endpoint must address a series of efficiency bottlenecks that extend beyond LLM inference. We then propose ScaleLLM, an optimized system for resource-efficient LLM serving. Our extensive experiments reveal that with 64 concurrent requests, ScaleLLM achieves a 4.3x speed up over vLLM and outperforms state-of-the-arts with 1.5x higher throughput.

Transfer learning via fine-tuning pre-trained transformer models has gained significant success in delivering state-of-the-art results across various NLP tasks. In the absence of centralized data, Federated Learning (FL) can benefit from distributed and private data of the FL edge clients for fine-tuning. However, due to the limited communication, computation, and storage capabilities of edge devices and the huge sizes of popular transformer models, efficient fine-tuning is crucial to make federated training feasible. This work explores the opportunities and challenges associated with applying parameter efficient fine-tuning (PEFT) methods in different FL settings for language tasks. Specifically, our investigation reveals that as the data across users becomes more diverse, the gap between fully fine-tuning the model and employing PEFT methods widens. To bridge this performance gap, we propose a method called SLoRA, which overcomes the key limitations of LoRA in high heterogeneous data scenarios through a novel data-driven initialization technique. Our experimental results demonstrate that SLoRA achieves performance comparable to full fine-tuning, with significant sparse updates with approximately sim 1% density while reducing training time by up to 90%.